Try a simple program with no user input apart from pressing the Arduino reset button. And with the stepper motors enabled all the time.
Get it to move enough steps for (say) 50mm of movement out an back with a short pause when the direction changes. It should be back at the original position. If it is not tell us the amount of error for each run of (say) 10 tests.
I have a really cheap Sieg C1 lathe to which I attached stepper motors. When I build an allowance for backlash into my program the error is less than 0.05mm as measured with a dial test indicator.
It is a complete waste of your time to try alternative enable modes until after you get the precision you want when the motors are permanently enabled.
...R